X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FHiddenColumns.java;h=fd4a9b5493f56348c130af1cb92eeec99695d007;hb=ecdbc96815298ac853543640881ef8d2384b48a1;hp=9a8669f0b863aa9d8c4c96eb4f048969d22990c1;hpb=9e064d395de4746f14106c1c296bc94696a6190e;p=jalview.git

diff --git a/src/jalview/datamodel/HiddenColumns.java b/src/jalview/datamodel/HiddenColumns.java
index 9a8669f..fd4a9b5 100644
--- a/src/jalview/datamodel/HiddenColumns.java
+++ b/src/jalview/datamodel/HiddenColumns.java
@@ -171,7 +171,8 @@ public class HiddenColumns
       if (!hiddenColumns.isEmpty())
       {
         // set up cursor reset values
-        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start);
+        HiddenCursorPosition cursorPos = cursor.findRegionForColumn(start,
+                false);
         regionindex = cursorPos.getRegionIndex();
 
         if (regionindex > 0)
@@ -356,7 +357,7 @@ public class HiddenColumns
 
       if (!hiddenColumns.isEmpty())
       {
-        int regionIndex = cursor.findRegionForColumn(start)
+        int regionIndex = cursor.findRegionForColumn(start, false)
                 .getRegionIndex();
 
         if (regionIndex != -1 && regionIndex != hiddenColumns.size())
@@ -544,7 +545,8 @@ public class HiddenColumns
 
       if (!hiddenColumns.isEmpty())
       {
-        result += cursor.findRegionForVisColumn(column).getHiddenSoFar();
+        result += cursor.findRegionForColumn(column, true)
+                .getHiddenSoFar();
       }
 
       return result;
@@ -574,7 +576,7 @@ public class HiddenColumns
       if (!hiddenColumns.isEmpty())
       {
         HiddenCursorPosition cursorPos = cursor
-                .findRegionForColumn(hiddenColumn);
+                .findRegionForColumn(hiddenColumn, false);
         int index = cursorPos.getRegionIndex();
         int hiddenBeforeCol = cursorPos.getHiddenSoFar();
     
@@ -656,7 +658,8 @@ public class HiddenColumns
       LOCK.readLock().lock();
       if (!hiddenColumns.isEmpty())
       {
-        int index = cursor.findRegionForColumn(alPos).getRegionIndex();
+        int index = cursor.findRegionForColumn(alPos, false)
+                .getRegionIndex();
 
         if (left && index > 0)
         {
@@ -700,7 +703,8 @@ public class HiddenColumns
     {
       LOCK.readLock().lock();
 
-      int regionindex = cursor.findRegionForColumn(column).getRegionIndex();
+      int regionindex = cursor.findRegionForColumn(column, false)
+              .getRegionIndex();
       if (regionindex > -1 && regionindex < hiddenColumns.size())
       {
         int[] region = hiddenColumns.get(regionindex);
@@ -846,7 +850,7 @@ public class HiddenColumns
       
       if (!hiddenColumns.isEmpty())
       {
-        HiddenCursorPosition pos = cursor.findRegionForColumn(start);
+        HiddenCursorPosition pos = cursor.findRegionForColumn(start, false);
         int index = pos.getRegionIndex();
         int startindex = index; // first index in hiddenColumns to remove
 
@@ -863,7 +867,7 @@ public class HiddenColumns
           }
         }
 
-        pos = cursor.findRegionForColumn(end);
+        pos = cursor.findRegionForColumn(end, false);
         index = pos.getRegionIndex();
         int endindex = index - 1; // last index in hiddenColumns to remove
 
@@ -973,7 +977,7 @@ public class HiddenColumns
       if (!hiddenColumns.isEmpty())
       {
         // look for a region ending just before adjres
-        int regionindex = cursor.findRegionForColumn(adjres - 1)
+        int regionindex = cursor.findRegionForColumn(adjres - 1, false)
                 .getRegionIndex();
         if (regionindex < hiddenColumns.size()
                 && hiddenColumns.get(regionindex)[1] == adjres - 1)
@@ -1055,7 +1059,7 @@ public class HiddenColumns
       // region we'll get the cursor pointing to the region before, which is
       // what we want
       HiddenCursorPosition pos = cursor
-              .findRegionForColumn(absoluteStart - 1);
+              .findRegionForColumn(absoluteStart - 1, false);
 
       return new BoundedStartRegionIterator(pos, start, end,
               hiddenColumns);